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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SpatialDecon.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings SpatialDecon_1.5.5.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/SpatialDecon.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SpatialDecon/DESCRIPTION' ... OK
* this is package 'SpatialDecon' version '1.5.5'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'SpatialDecon' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
download_profile_matrix: no visible binding for global variable
  'profile_matrix'
Undefined global functions or variables:
  profile_matrix
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                                user system elapsed
runReverseDecon                                71.67   0.29   72.00
runReverseDecon-NanoStringGeoMxSet-method      68.69   0.47   69.16
runCollapseCellTypes                           65.17   0.64   65.81
runCollapseCellTypes-NanoStringGeoMxSet-method 63.83   0.52   64.39
runspatialdecon                                48.37   2.83   52.14
runspatialdecon-Seurat-method                  32.29   2.25   35.81
runspatialdecon-NanoStringGeoMxSet-method      16.23   0.07   16.29
runMergeTumorIntoX-NanoStringGeoMxSet-method   13.30   0.07   13.37
runErrorModel                                  12.83   0.05   12.87
runMergeTumorIntoX                             12.55   0.13   12.67
reverseDecon                                    5.92   0.03    5.96
SpatialDecon-package                            4.89   0.72    5.61
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/SpatialDecon.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL SpatialDecon
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'SpatialDecon' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SpatialDecon'
    finding HTML links ... done
    SpatialDecon-package                    html  
    TIL_barplot                             html  
    cellcols                                html  
    collapseCellTypes                       html  
    create_profile_matrix                   html  
    derive_GeoMx_background                 html  
    download_profile_matrix                 html  
    florets                                 html  
    mean.resid.sd                           html  
    mergeTumorIntoX                         html  
    mini_geomx_dataset                      html  
    mini_singleCell_dataset                 html  
    nsclc                                   html  
    reverseDecon                            html  
    runCollapseCellTypes-NanoStringGeoMxSet-method
                                            html  
    runCollapseCellTypes                    html  
    runErrorModel                           html  
    runMergeTumorIntoX-NanoStringGeoMxSet-method
                                            html  
    runMergeTumorIntoX                      html  
    runReverseDecon-NanoStringGeoMxSet-method
                                            html  
    runReverseDecon                         html  
    runspatialdecon-NanoStringGeoMxSet-method
                                            html  
    runspatialdecon-Seurat-method           html  
    runspatialdecon                         html  
    safeTME                                 html  
    safeTME.matches                         html  
    spatialdecon                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SpatialDecon)
Making 'packages.html' ... done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(SpatialDecon)
> 
> test_check("SpatialDecon")
[1] "Creating Atlas"
[1] "1 / 4 : B"
[1] "2 / 4 : C"
[1] "3 / 4 : A"
[1] "4 / 4 : D"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 85 ]
> 
> proc.time()
   user  system elapsed 
 183.37    2.43  188.65